This invention relates to seco-cyclopropapyrroloindole compounds, conjugates thereof, and methods of making and using such compounds and conjugates.
Double helical DNA has two longitudinal spiral grooves running along its exterior, much like the stripes on a barbershop pole. The two grooves are not identical: one, called the major groove, is much wider than the other, called the minor groove.
The width of the minor groove is approximately equal to the thickness of a benzene ring. Many biologically active DNA-binding molecules are substantially planar polyaromatic molecules having an arcuate footprint, such shape enabling them to slide snugly in the minor groove. One class of these molecules not only bind to DNA, but also alkylate it and are referred to as DNA minor groove binder-alkylators (“MGBAs”).
An MGBA subclass is represented by the natural products CC-1065, duocarmycin SA, and yatakemycin (Boger and Johnson 1995; Tichenor et al. 2007). (Full citations for the documents cited herein by first author or inventor and year are listed at the end of this specification.) They comprise an alkylating subunit and one or more binding subunits, the latter contributing to binding to DNA but being chemically unreactive towards it. In CC-1065 and duocarmycin SA, the alkylating subunit is at one end of the molecule and the binding subunit(s) are at the other end. In yatakemycin, the alkylating subunit is flanked by binding subunits. Consonant with the overall MGBA architecture, the alkylating and binding subunits themselves are polyaromatic and substantially planar. As the alkylating subunit has a cyclopropapyrrolo-indole (“CPI”) core structure, MGBAs in this subclass are eponymously named CPI compounds.

Upon binding to DNA, the CPI cyclopropyl ring is activated and alkylates DNA at an adenine N3 nitrogen (Hurley et al. 1984). One theory proposed to explain the activation is that binding introduces further conformational strain into the already-strained cyclopropyl ring, increasing its reactivity (Boger 2001; Boger et al. 1997; Tichenor et al. 1997).

Seco-CPI compounds are variants of CPI compounds in which the cyclopropyl ring has been opened and replaced with a halomethyl group. While seco-CPI compounds themselves do not alkylate DNA, they are readily convertible in vitro or in vivo to CPI compounds and their biological activity is essentially the same as the latter's (Li et al. 2012). Thus, seco-CPI compounds are of interest as synthetically convenient functional equivalents of CPI compounds or as intermediates for their synthesis (Boger et al. 2000).

An advantage of a seco-CPI compound is that it can be prodrugged to control conversion to the CPI form. Attaching a prodrugging group PD to the phenolic hydroxyl group prevents conversion to the CPI form unless PD is cleaved off first. PD can be chosen such that it is cleaved by an agent found at or near the site of intended biological action, such as a tumor, to reduce the risk of systemic toxicity. PD preferably is an enzymatically cleavable group, such as a carbamate, phosphate, glycoside, or glucuronide, which are cleavable by carboxyesterase, phosphatase, glycosidase, or glucuronidase, respectively. See, e.g., Kobayashi et al. 1994; Lajiness et al. 2010; Sufi et al. 2013; Tietze et al. 2001; Zhang et al. 2014.

Studies on analogs of CPI compounds led to the development of another MGBA subclass, in which the CPI pyrrole group is replaced by a benzene ring. Such compounds are called CBI compounds, after the cyclopropabenzindole (“CBI”) core of the alkylating subunit. Like CPI compounds, CBI compounds can exist in seco and prodrugged seco forms. The simpler CBI structure is more accessible synthetically and CBI compounds have been shown to be both stable and biologically potent (Lajiness et al. 2010; Boger et al. 1990 and 1999).

Both CPI and CBI compounds are potent cytotoxins, making them attractive candidates as anti-cancer agents. Substantial research efforts have been dedicated to synthesizing and evaluating such compounds and their seco variants for such use. See, e.g., Boger 2003; Kobayashi et al. 1994; Li et al. 1992; Nagamura and Saito 1998; Nagamura et al. 1996; Tichenor et al. 2007; Tietze et al. 2008.
A type of anticancer agent that is generating strong interest is a conjugate, in which a drug is attached to a targeting agent that binds to a ligand on the cancer cell. The targeting agent thus directs the drug to the cancer cell, where it is released by one of several mechanisms to act on the cancer cell.
A common type of conjugate is an antibody-drug conjugate (ADC, also referred to as an immunoconjugate). In an ADC, a drug (also referred to as a therapeutic agent, cytotoxin, payload, or warhead) is covalently linked to an antibody whose antigen is a tumor associated antigen—i.e., an antigen expressed by a cancer cell.
The moiety covalently linking the antibody and the drug is referred to as the linker. Where each antibody has one drug attached to it, the structure of an ADC can be represented as:[Antibody]-[Linker]-[Drug]
The antibody, upon binding to the antigen, delivers the ADC to the cancer site. There, cleavage of the linker or degradation of the antibody releases the drug. Frequently, the ADC is internalized by endocytosis into the target cell and release of the drug takes place inside it. While the ADC is circulating in the blood, the drug is held inactive because of its linkage to the antibody. Consequently, the drug in an ADC can be much more potent (cytotoxic) than an ordinary chemotherapy agent because its localized release reduces systemic toxicity. For a review on ADCs, see Schrama et al. 2006.
CPI and CBI compounds, along with their seco counterparts, have been proposed as the drug in an ADC. See, for example, Boyd et al. 2008; Chari et al. 1995; Chen et al. 2014; Ducry et al. 2010; Gangwar et al. 2011; Ng et al. 2006, 2009, and 2011; Sufi et al. 2013; Zhang et al. 2014; Zhao et al. 2010.